牛北方
牛北方
博士生导师
岗位:研究员
职务:高性能计算部副主任/计算基因组学实验室主任
所属部门:高性能计算技术与应用发展部
学历:博士研究生
邮箱:niubf@cnic.cn
通讯地址:
学科专业(学术型/专业型):计算机软件与理论,电子信息
招生方向:高性能计算与生物信息学
承担科研项目等情况
先后承担了国家重点研发计划、国家自然科学基金、中国科学院战略性先导科技专项等10余项课题/项目,在Nature、Nature Genetics等国际重要科技期刊发表SCI检索论文62篇,被引用19000多次(H-index为32,Google Scholar数据)。
代表性工作包括提出了基因组微卫星不稳定性(MSI)信号精准探测的新方法,形成了国际上具有核心地位的肿瘤样本多层次临床应用场景的MSI算法体系MSIsensor/MSIsensor2/MSIsensor-ct,并被成功应用于美国FDA批准的首个NGS肿瘤基因检测平台(MSK-IMPACT),同时被近期发布的2021版《结直肠癌分子检测高通量测序中国专家共识》所推荐。
目前该系列算法被超过27个国家的670个临床研究项目所应用,推动了肿瘤免疫治疗领域的研究进展,为人类癌症的精准诊治做出了一定贡献。
曾获2015年美国10大临床研究成就奖(Top 10 Clinical Research Achievement Awards for 2015)。 
代表论著

[1]. Xinyin Han*, Shuying Zhang*, Daniel Cui Zhou, Dongliang Wang, Xiaoyu He, Danyang Yuan, Ruilin Li, Jiayin He, Xiaohong Duan, Michael C Wendl, Li Ding#, Beifang Niu#. (2021). MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. Briefings in Bioinformatics, bbaa402, https://doi.org/10.1093/bib/bbaa402

[2]. Xiaoyu He, Yu Zhang, Danyang Yuan, Xinyin Han, Jiayin He, Xiaohong Duan, Siyao Liu, Xintong Wang, Beifang Niu#. (2021). DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation. Frontiers in Oncology, 11: 672597.

[3]. Danyang Yuan, Xiaoyu He, Xinyin Han, Chunyan Yang, Fei Liu, Shuying Zhang, Haijing Luan, Ruilin Li, Jiayin He, Xiaohong Duan, Dongliang Wang, Qiming Zhou, Sujun Gao #, Beifang Niu#. (2021). Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. Briefings in Bioinformatics, bbab099, https://doi.org/10.1093/bib/bbab099

[4]. Xiaoyu He, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, Beifang Niu#. (2020). Comprehensive fundamental analysis and quality management strategy for next-generation sequencing data from cancer genomes. Briefings in Bioinformatics, bbaa083, https://doi.org/10.1093/bib/bbaa083

[5]. Shanyu Chen, Xiaoyu He, Ruilin Li, Xiaohong Duan, Beifang Niu#. (2020). HotSpot3D web server: An Integrated Resource for Mutation Analysis in Protein 3D Structures. Bioinformatics, 36(12): 3944-3946.

[6]. Liping Sun, Yang Yu, Beifang Niu#, Deqing Wang#. (2020). Red blood cells may act as repositories of microRNAs in the circulatory system. Frontiers in Genetics, 11: 442.

[7]. Chuangchuang Dai, Haijing Luan, Qingbing Yu, Xiaoyu He, Yunhao Wang, Bincheng Shuai, Xiaobing Guo#, Zhonghua Lu#, Beifang Niu#. (2020, August). Change-Encryption: Encryption Using Spatiotemporal Information as a Function Model. In 2020 7th IEEE International Conference on Cyber Security and Cloud Computing (CSCloud)/ 6th IEEE International Conference on Edge Computing and Scalable Cloud (EdgeCom) (pp. 281-287).

[8]. Chuangchuang Dai, Xueying Yang, Meikang Qiu, Xiaobing Guo#, Zhonghua Lu#, Beifang Niu#. (2020, September). Digital Currency Investment Strategy Framework Based on Ranking. In Algorithms and Architectures for Parallel Processing (ICA3PP 2020) (pp. 654-662).

[9]. Ruilin Li, Xiaoyu He, Chuangchuang Dai, Haidong Zhu, Xianyu Lang, Wei Chen, Xiaodong Li, Dan Zhao, Yu Zhang, Xinyin Han, Tie Niu, Yi Zhao, Rongqiang Cao, Rong He, Zhonghua Lu, Xuebin Chi, Weizhong Li#, Beifang Niu#. (2019). Gclust: A Parallel Clustering Tool for Microbial Genomic Data. Genomics, Proteomics & Bioinformatics, 17(5): 496-502.

[10]. Shanyu Chen, Zhipeng He, Xinyin Han, Xiaoyu He, Ruilin Li, Haidong Zhu, Dan Zhao, Chuangchuang Dai, Yu Zhang, Zhonghua Lu, Xuebin Chi, Beifang Niu#. (2019). How Big Data and High-performance Computing Drive Brain Science. Genomics, Proteomics & Bioinformatics, 17(4): 381-392.

[11]. Zekun Yin, Xiaoming Xu, Kaichao Fan, Ruilin Li, Weizhong Li, Weiguo Liu#, Beifang Niu#. (2019, November). DGCF: A Distributed Greedy Clustering Framework for Large-scale Genomic Sequences. In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 2272-2279). IEEE.

[12]. Shuo Li, Zhonghua Lu, Yongze Sun, Sungen Deng, Beifang Niu#. (2019, May). Distributed Parameter Optimization Scheduling Strategy and System Design Based on Mesos. In 2019 IEEE 5th Intl Conference on Big Data Security on Cloud (BigDataSecurity), IEEE Intl Conference on High Performance and Smart Computing, (HPSC) and IEEE Intl Conference on Intelligent Data and Security (IDS) (pp. 218-224). IEEE.

[13]. Wei Zhou*, Ruilin Li*, Shuo Yuan, ChangChun Liu, Shaowen Yao, Jing Luo#, Beifang Niu#. (2017). MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes. Bioinformatics, 33(7): 1090-1092.

[14]. Beifang Niu*, Adam D. Scott*, Sohini Sengupta*, Matthew H. Bailey, Prag Batra, Jie Ning, Matthew A. Wyczalkowski, Wen-Wei Liang, Qunyuan Zhang, Michael D. McLellan, Sam Q. Sun, Piyush Tripathi, Carolyn Lou, Kai Ye, Robert J. Mashl, John Wallis, Michael C. Wendl, Feng Chen#, Li Ding#. (2016). Protein-structure-guided discovery of functional mutations across 19 cancer types. Nature Genetics, 48(8): 827-837.

[15]. Beifang Niu*, Kai Ye*, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl and Li Ding#. (2014). MSIsensor: microsatellite instability detection using paired tu-mor-normal sequence data. Bioinformatics, 30(7):1015-6.

[16]. Beifang Niu, Zhengwei Zhu, Limin Fu, Sitao Wu, Weizhong Li#. (2011). FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Bioinformatics, 27(12): 1704-1705.

[17]. Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li#. (2010). Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics, 11:187.

[18]. Beifang Niu#, Xianyu Lang, Zhonghua Lu, Xuebin Chi. (2009). Parallel algorithm research on several important open problems in bioinformatics. Interdisciplinary Sciences: Computational Life Sciences, 1(3): 187-195.

[19]. Beifang Niu#, Xianyu Lang, Zhonghua Lu, Xuebin Chi. (2007). ScBioGrid: a commodity supercomputing environment supporting bioinformatics research. International Journal of Computer Mathematics, 84(2):177-182.

[20]. Zekun Yin#, Hao Zhang#, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu#. (2020). RabbitQC: high-speed scalable quality control for sequencing data. Bioinformatics, 37(4): 573-574.

[21]. Junlan Zhu, Zhongxian Tian, Yang Li, Xiaohui Hua, Dongyun Zhang, Jingxia Li, Honglei Jin, Jiheng Xu, Wei Chen, Beifang Niu, Xue-Ru Wu, Sergio Comincini, Haishan Huang#, Chuanshu Huang#. (2019). ATG7 Promotes Bladder Cancer Invasion via Autophagy‐Mediated Increased ARHGDIB mRNA Stability. Advanced Science, 6(8): 1801927.

[22]. Liping Sun, Fengyan Fan, Ruilin Li, Beifang Niu, Liguo Zhu, Shuai Yu, Shuying Wang, Cuiying Li# and Deqing Wang#. (2018). Different Erythrocyte MicroRNA Profiles in Low- and High-Altitude Individuals. Frontiers in Physiology, 9: 1099.

[23]. Yanan Cao#, Weiwei Zhou, Lin Li, Jiaqian Wang, Zhibo Gao, Yiran Jiang, Xiuli Jiang, Aijing Shan, Matthew H. Bailey, Kuan-lin Huang, Sam Q. Sun, Michael D. McLellan, Beifang Niu, Weiqing Wang, Li Ding#, Guang Ning#. (2018). Pan-Cancer Analysis of Somatic Mutations Across 21 Neuroendocrine Tumor Types. Cell Research, 28(5): 601-604.

[24]. Robert J Mashl*, Adam D Scott, Kuan-lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Feny?, Benjamin Raphael, Michael C Wendl, Li Ding#. (2017). GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Research, 27(8): 1450-1459.

[25]. Kuan-lin Huang*, Shunqiang Li*, Philipp Mertins*, Song Cao, Harsha P Gunawardena, Kelly V Ruggles, DR Mani, Karl R Clauser, Maki Tanioka, Jerry Usary, Shyam M Kavuri, Ling Xie, Christopher Yoon, Jana W Qiao, John Wrobel, Matthew A Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E Snider, Jeremy Hoog, Purba Singh, Beifang Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D McLellan, Michael C Wendl, Anna Malovannaya, Jason M Held, Michael A Gillette, David Feny?, Christopher R Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R Davies, Charles M Perou, Cynthia Ma, R Reid Townsend, Xian Chen, Steven A Carr, Matthew J Ellis, Li Ding#. (2017). Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nature Communications, 8: 14864.

[26]. Song Cao, Michael C. Wendl, Matthew A. Wyczalkowski, Kristine Wylie, Kai Ye, Reyka Jayasinghe, Mingchao Xie, Song Wu, Beifang Niu, Robert Grubb III, Kimberly J. Johnson, Hiram Gay, Ken Chen, Janet S. Rader, John F. Dipersio, Feng Chen, Li Ding#. (2016). Divergent viral presentation among human tumors and adjacent normal tissues. Scientific Reports, 6: 28294.

[27]. Kai Ye*, Jiayin Wang*, Reyka Jayasinghe, Eric-Wubbo Lameijer, Joshua F McMichael, Jie Ning, Michael D McLellan, Mingchao Xie, Song Cao, Venkata Yellapantula, Kuan-lin Huang, Adam Scott, Steven Foltz, Beifang Niu, Kimberly J Johnson, Matthijs Moed, PEline Slagboom, Feng Chen, Michael C Wendl, Li Ding#. (2015). Systematic discovery of complex insertions and deletions in human cancers. Nature Medicine, 22(1): 97-104.

[28]. Charles Lu*, Mingchao Xie*, Michael C. Wendl, Jiayin Wang, Michael D. McLellan, Mark D. M. Leiserson, Kuan-lin Huang, Matthew A. Wyczalkowski, Reyka Jayasinghe, Tapahsama Banerjee, Jie Ning, Piyush Tripathi, Qunyuan Zhang, Beifang Niu, Kai Ye, Heather K. Schmidt, Robert S. Fulton,Joshua F. McMichael, Prag Batra, Cyriac Kandoth, Maheetha Bharadwaj, Daniel C. Koboldt, Christopher A. Miller, Krishna L. Kanchi, James M. Eldred, David E. Larson, John S. Welch, Ming You, Bradley A. Ozenberger, Ramaswamy Govindan, Matthew J. Walter, Matthew J. Ellis, Elaine R. Mardis, Timothy A. Graubert, John F. Dipersio, Timothy J. Ley, Richard K. Wilson, Paul J. Goodfellow, Benjamin J. Raphael, Feng Chen, Kimberly J. Johnson, Jeffrey D. Parvin, Li Ding#. (2015). Patterns and functional implications of rare germline variants across 12 cancer types. Nature Communications, 6: 10086.

[29]. Mark DM Leiserson*, Fabio Vandin*, Hsin-Ta Wu, Jason R Dobson, Jonathan V Eldridge, Jacob L Thomas, Alexandra Papoutsaki, Younhun Kim, Beifang Niu, Michael McLellan, Michael S Lawrence, Abel Gonzalez-Perez, David Tamborero, Yuwei Cheng, Gregory A Ryslik, Nuria Lopez-Bigas, Gad Getz, Li Ding, Benjamin J Raphael#. (2015). Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes. Nature Genetics, 47(2): 106-144.

[30]. Katherine A Hoadley*, Christina Yau*, Denise M Wolf*, Andrew D Cherniack*, David Tamborero, Sam Ng, Max DM Leiserson, Beifang Niu, Michael D McLellan, Vladislav Uzunangelov, Jiashan Zhang, Cyriac Kandoth, Rehan Akbani, Hui Shen, Larsson Omberg, Andy Chu, Adam A Margolin, Laura J van’t Veer, Nuria Lopez-Bigas, Peter W Laird, Benjamin J Raphael, Li Ding, A Gordon Robertson, Lauren A Byers, Gordon B Mills, John N Weinstein, Carter Van Waes, Zhong Chen, Eric A Collisson, Christopher C Benz#, Charles M Perou#, Joshua M Stuart#, Cancer Genome Atlas Research Network. (2014). Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158(4): 929-944.

[31]. Cyriac Kandoth*, Michael D McLellan*, Fabio Vandin, Kai Ye, Beifang Niu, Charles Lu, Mingchao Xie, Qunyuan Zhang, Joshua F McMichael, Matthew A Wyczalkowski, Mark DM Leiserson, Christopher A Miller, John S Welch, Matthew J Walter, Michael C Wendl, Timothy J Ley, Richard K Wilson, Benjamin J Raphael, Li Ding#. (2013). Mutational landscape and significance across 12 major cancer types. Nature, 502 (7471): 333-339.

[32]. Ken Chen#, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D Mclellan, Katherine A Hoadley, Elaine R Mardis, Timothy J Ley, Charles M Perou, Richard K Wilson, Li Ding#. (2013). BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biology, 14(8): R87.

[33]. Matthew J. Walter*, Dong Shen*, Jin Shao*, Li Ding, Brian White, Cyriac Kandoth, Christopher A. Miller, Beifang Niu, Michael D. McLellan, Nathan D. Dees, Robert Fulton, Kevin Elliot, Sharon Heath, Marcus Grillot, Peter Westervelt, Daniel C. Link, John F. DiPersio, Elaine Mardis, Timothy J. Ley, Richard K. Wilson, Timothy A. Graubert#. (2013). Clonal Diversity of Recurrently Mutated Genes in Myelodysplastic Syndromes. Leukemia, 27: 1275–1282.

[34]. Zhengwei Zhu*, Beifang Niu, Sitao Wu, Weizhong Li#. (2013). MGAviewer: A desktop visualization tool for analysis of metage-nomics alignment data. Bioinformatics, 29(1): 122-123.

[35]. Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu and Weizhong Li#. (2012). CD-HIT: accelerated for clustering the next generation sequencing data. Bioinformatics, 28(23): 3150–3152.

[36]. Weizhong Li#, Limin Fu, Beifang Niu, Sitao Wu, John Wooley. (2012). Ultrafast clustering algorithms for metagenomic sequence analysis. Briefings in Bioinformatics, 13 (6): 656-668.

[37]. Sitao Wu, Zhengwei Zhu, Limin Fu, Beifang Niu, Weizhong Li#. (2011). WebMGA: a Customizable Web Server for Fast Metagenomic Sequence Analysis. BMC Genomics, 12: 444.

[38]. Ying Huang, Beifang Niu, Ying Gao, Limin Fu, Weizhong Li#. (2010). CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26(5): 680–682.

[39]. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793): 82-93.

[40]. Ludmil B. Alexandrov,…, Michael R. Stratton#, PCAWG Consortium. (2020). The repertoire of mutational signatures in human cancer. Nature, 578(7793): 94-101.

[41]. Esther Rheinbay,…, Gad Getz#, PCAWG Consortium. (2020). Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578(7793): 102-111.

[42]. Yilong Li,…,Peter J. Campbell#, PCAWG Consortium. (2020). Patterns of somatic structural variation in human cancer genomes. Nature, 578(7793): 112-121.

[43]. Moritz Gerstung#,…, PCAWG Consortium. (2020). The evolutionary history of 2,658 cancers. Nature, 578(7793): 122-128.

[44]. PCAWG Transcriptome Core Group,…, PCAWG Consortium. (2020). Genomic basis for RNA alterations in cancer. Nature, 578(7793): 129-136.

[45]. Sergei Yakneen#,…, PCAWG Consortium. (2020). Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 38(3): 288-292.

[46]. Kadir C. Akdemir,…, PCAWG Consortium. (2020). Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics, 52(3): 294-305.

[47]. Bernardo Rodriguez-Martin,…, PCAWG Consortium. (2020). Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics, 52(3): 306-319.

[48]. Marc Zapatka,…, PCAWG Consortium. (2020). The landscape of viral associations in human cancers. Nature Genetics, 52(3): 320-330.

[49]. Isidro Cortés-Ciriano,…, PCAWG Consortium. (2020). Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics, 52(3): 331-341.

[50]. Yuan Yuan,…, PCAWG Consortium.(2020). Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers. Nature Genetics, 52(3): 342-352.

[51]. Matthew H. Bailey,…, PCAWG Consortium. (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11:4748.

[52]. Constance H. Li,…, PCAWG Consortium. (2020). Sex differences in oncogenic mutational processes. Nature Communications, 11:4330.

[53]. Wei Jiao,…, PCAWG Consortium. (2020). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications, 11: 728.

[54]. Matthew A. Reyna, …, PCAWG Consortium. (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications, 11: 729.

[55]. Marek Cmero#, …, PCAWG Consortium. (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11: 730.

[56]. Yulia Rubanova,…, PCAWG Consortium. (2020). Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature Communications, 11: 731.

[57]. Lina Sieverling,…, PCAWG Consortium. (2020). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications, 11: 733.

[58]. Shimin Shuai#,…, PCAWG Consortium. (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11: 734.

[59]. Marta Paczkowska, …, PCAWG Consortium. (2020). Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11: 735.

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[61]. Vinayak Bhandari,…, PCAWG Consortium. (2020). Divergent mutational processes distinguish hypoxic and normoxic tumours. Nature Communications, 11(1): 737.

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